So apparently (being a linux novice) I didn't realize it was insufficient to
simply have the file marked as executable. It turns out the default TMP
directory on my machine is mounted with a noexec flag so no files in that
directory are allowed to be executed. The solution is to set an environment
variable TMPDIR=some new directory I created (eg. /home/myusername/tmp) Then R
uses that directory for the installs. The easiest method then is to use do
sudo R
Sys.setev(TMPDIR="/home/myusername/tmp")
install.packages(pkglist)
the sudo R part just ensures I am installing into the global library and not a
user specific library
--
W. Michael Conklin
EVP Marketing & Data Sciences
GfK
T +1 763 417 4545 | M +1 612 567 8287
-----Original Message-----
From: Conklin, Mike (GfK)
Sent: Friday, June 23, 2017 4:38 PM
To: Don Cohen; Duncan Murdoch
Cc: Martin Maechler; r-help at r-project.org
Subject: Re: [R] Missing dependencies in pkg installs
Checked all the permissions, and it appears that file_test returns a FALSE and
system(ls -l) shows it is executable, so the problem seems to be in R and
it's relationship to RHEL. I tried installing R3.3.3 to see if the older
version would install stringi and had the same problem so it doesn't appear
to be R3.4 related. I am now reaching out to some other sources who may have
installed R on similar systems.
________________________________________
From: Conklin, Mike (GfK)
Sent: Friday, June 23, 2017 8:50 AM
To: Don Cohen; Duncan Murdoch
Cc: Martin Maechler; r-help at r-project.org
Subject: RE: [R] Missing dependencies in pkg installs
I had the same thought in the shower this morning but I was disappointed to find
that SElinux was disabled on the system. My next step will be to install a
previous version of R on the system. My problem is that I am planning a shiny
server installation and at least half of the apps on the current system depend
on these libraries that will not install.
--
W. Michael Conklin
EVP Marketing & Data Sciences
GfK
T +1 763 417 4545 | M +1 612 567 8287
-----Original Message-----
From: Don Cohen [mailto:don-r-help at isis.cs3-inc.com]
Sent: Thursday, June 22, 2017 6:18 PM
To: Duncan Murdoch
Cc: Conklin, Mike (GfK); Martin Maechler; r-help at r-project.org
Subject: Re: [R] Missing dependencies in pkg installs
Duncan Murdoch writes:
> On 22/06/2017 5:02 PM, Conklin, Mike (GfK) wrote:
> > I am using debug on the .install_packages function...stepping
through. Once the temporary folder is created and the tar file expanded I run
file_test and get a FALSE back indicating that the configure file is not
executable.
>
> I don't know what is causing this bug. Perhaps a Linux user can >
reproduce it and fix it.
>
> Here's what I see:
>
> file_test("-x") calls file.access(filename, 1L). That in turn
calls the > C library function access(..., X_OK). The ... is the name of
the file, > translated into the local encoding and expanded. As far as I
can see, > that means ... should be exactly the string below.
> >
> > [1] "/tmp/RtmpMM6iC1/R.INSTALLc5ca415e4310/stringi"
>
> The only thing I can think of is that your system is protecting you from
> executing a newly created file until some sort of virus or other check
> is done. (This is common on Windows, but I've never heard of it before
> on Linux.)
Just a thought - are you running SELinux ?
Check the log files for refusals to run programs.
